Genetics and Genomics Commons^™

Diversity Of Trna Clusters In The Chloroviruses, Garry A. Duncan, David D. Dunigan Ph. D., James L. Van Etten

Nebraska Center for Virology: Faculty Publications

Viruses rely on their host’s translation machinery for the synthesis of their own proteins. Problems belie viral translation when the host has a codon usage bias (CUB) that is different from an infecting virus due to differences in the GC content between the host and virus genomes. Here, we examine the hypothesis that chloroviruses adapted to host CUB by acquisition and selection of tRNAs that at least partially favor their own CUB. The genomes of 41 chloroviruses comprising three clades, each infecting a different algal host, have been sequenced, assembled and annotated. All 41 viruses not only encode tRNAs, but …

Comparison Of Poly-A+ Selection And Rrna Depletion In Detection Of Lncrna In Two Equine Tissues Using Rna-Seq, Anna R. Dahlgren, Erica Y. Scott, Tamer Mansour, Erin N. Hales, Pablo J. Ross, Theodore S. Kalbfleisch, James N. Macleod, Jessica Lynn Petersen, Rebecca R. Bellone, Carrie J. Finno

Department of Animal Science: Faculty Publications

Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A+ selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which library preparation method is optimal for lncRNA investigations in the horse. Using liver and cerebral parietal lobe tissues from two …

Special Topic: Cell-Based Meat: The Need To Assess Holistically, Cameron Faustman, Deb Hamernik, Michael Looper, Steven A. Zinn

Department of Animal Science: Faculty Publications

Proof-of-principle for large-scale engineering of edible muscle tissue, in vitro, was established with the product’s introduction in 2013. Subsequent research and commentary on the potential for cell-based meat to be a viable food option and potential alternative to conventional meat have been significant. While some of this has focused on the biology and engineering required to optimize the manufacturing process, a majority of debate has focused on cultural, environmental, and regulatory considerations. Animal scientists and others with expertise in muscle and cell biology, physiology, and meat science have contributed to the knowledge base that has made cell-based meat possible and …

Asas Celebrates 10 Years Of Publishing Animal Frontiers: The Review Magazine Of Animal Agriculture, Debora L. Hamernik, Meghan Wulster-Radcliffe, Steven A. Zinn

Department of Animal Science: Faculty Publications

In July 2011, the first issue of Animal Frontiers was published by an international consortium including the American Society of Animal Science (ASAS), the Canadian Society of Animal Science (CSAS), and the European Federation of Animal Science (EAAP). Development of an international, science-based, open access journal that provided review articles and global perspectives on the complex dynamics associated with the production of animal-sourced foods was an accomplishment in and of itself, but the ability to meet the needs of a diverse community of readers, including scientists, policy makers, educators, and the general public set Animal Frontiers apart from other journals. …

The Effect Of Varicocele On Semen Quality In Boars Exposed To Heat Stress, Tasha R. Gruhot, Brett White, Benny Mote

Department of Animal Science: Faculty Publications

Semen quality has a dramatic impact on reproductive efficiency in the swine industry, influencing both conception rate and litter size. The objective of this study was to assess whether the presence of varicocele hinders semen quality in both thermoneutral and heat stress (HS) conditions. At approximately 6 mo of age, ultrasonography was used to measure left and right pampiniform plexus area in order to detect varicocele in maternal line boars at the University of Nebraska–Lincoln. Between 10 and 12 mo of age, semen was collected from each boar (n = 28) twice weekly. Boars were collected under thermoneutral conditions, were …

Formation And Characterization Of Lipid Droplets Of The Bovine Corpus Luteum, Heather A. Talbott, Michele R. Plewes, Crystal Krause, Xiaoying Hou, Pan Zhang, William B. Rizzo, Jennifer R. Wood, Andrea S. Cupp, John S. Davis

Department of Animal Science: Faculty Publications

Establishment and maintenance of pregnancy depends on progesterone synthesized by luteal tissue in the ovary. Our objective was to identify the characteristics of lipid droplets (LDs) in ovarian steroidogenic cells. We hypothesized that LDs are a major feature of steroidogenic luteal cells and store cholesteryl esters. Whole bovine tissues, isolated ovarian steroidogenic cells (granulosa, theca, small luteal, and large luteal), and isolated luteal LDs were assessed for LD content, LD-associated proteins and lipid analyses. Bovine luteal tissue contained abundant lipid droplets, LD-associated perilipins 2/3/5, hormone-sensitive lipase, and 1-acylglycerol-3-phosphate O-acyltransferase ABHD5. Luteal tissue was enriched in triglycerides (TGs) compared to other …

Asas-Nanp Symposium: Ruminant/ Nonruminant Feed Composition: Challenges And Opportunities Associated With Creating Large Feed Composition Tables, Andres Schlageter-Tello, George C. Fahey, Tarra Freel, Liz Koutsos, Phillip S. Miller, William P. Weiss

Department of Animal Science: Faculty Publications

Traditional feed composition tables have been a useful tool in the field of animal nutrition throughout the last 70 yr. The objective of this paper is to discuss the challenges and opportunities associated with creating large feed ingredient composition tables. This manuscript will focus on three topics discussed during the National Animal Nutrition Program (NANP) Symposium in ruminant and nonruminant nutrition carried out at the American Society of Animal Science Annual Meeting in Austin, TX, on July 11, 2019, namely: 1) Using large datasets in feed composition tables and the importance of standard deviation in nutrient composition as well as …

Impact Of Cow Milk Production On Cow–Calf Performance In The Nebraska Sandhills, Tasha M. King, Jacki A. Musgrave, Richard N. Funston, J. Travis Mulliniks

Department of Animal Science: Faculty Publications

Livestock producers have tended to select for increased output traits like milk production and growth to increase productivity. Even with the increased selection for greater calf growth potential, some regions in the United States have seen a plateau in calf body weight (BW) at weaning (Lalman et al., 2019). When focusing on reaching maximum potential of these output traits, it is important to consider the multitude of variables that affect a production system. With increased milk production, nutrient requirements for cows become increased (Ferrell and Jenkins, 1984; Montaño-Bermudez et al., 1990), which may not be met if range and forage …

Influence Of Host Genetics In Shaping The Rumen Bacterial Community In Beef Cattle, Waseem Abbas, Jeremy T. Howard, Henry Paz, Kristin E. Hales, James E. Wells, Larry A. Kuehn, Galen E. Erickson, Matthew L. Spangler, Samodha Fernando

Department of Animal Science: Faculty Publications

In light of recent host-microbial association studies, a consensus is evolving that species composition of the gastrointestinal microbiota is a polygenic trait governed by interactions between host genetic factors and the environment. Here, we investigated the effect of host genetic factors in shaping the bacterial species composition in the rumen by performing a genome-wide association study. Using a common set of 61,974 single-nucleotide polymorphisms found in cattle genomes (n = 586) and corresponding rumen bacterial community composition, we identified operational taxonomic units (OTUs), Families and Phyla with high heritability. The top associations (1-Mb windows) were located on 7 chromosomes. These …

Genetic Structure And Admixture In Sheep From Terminal Breeds In The United States, Kimberly M. Davenport, C. Hiemke, Stephanie D. Mc Kay, J. W. Thorne, Ronald M. Lewis, Todd Taylor, B. M. Murdoch

Department of Animal Science: Faculty Publications

Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright’s FST estimates and an identity by state matrix. …

Demonstrating Mate Choice Copying In Spiders Requires Further Research, R. Tucker Gilman, Kasey Fowler-Finn, Eileen A. Hebets

Eileen Hebets Publications

Mate choice copying—when individuals learn to prefer mates or mate types that have been chosen by others—can influence trait evo-lution and speciation (Varela et al. 2018; Dion et al. 2019). Most examples of mate choice copying are from fish, birds, and mammals including humans (Varela et al. 2018). However, 2 invertebrate examples—fruit flies and wolf spiders—have been used to argue that the phenomenon may be phylogenetically widespread, and perhaps the rule rather than the exception in nature (Varela et al. 2018). Here, we revisit the evidence for mate choice copying in wolf spiders (Fowler-Finn et al. 2015) in light of …

The Physical Interactions Of Klp-4 & The Effects Of Microtubule Acetylation, Lindsey Wright

Honors Program Theses

Our nervous system propagates signals by releasing neurotransmitters into the synaptic cleft between two adjacent neurons. The transport and delivery of such neurotransmitters within the neuron is reliant on microtubule structure and motor proteins present. The direction of motor protein transport is dictated by the inherent polarity of microtubules. Kinesin-3 motor proteins, such as KLP-4 found in Caenorhabditis elegans, use this polarity to travel in an anterograde direction towards neurotransmitter exocytosis sites. Thus, KLP-4 is associated with the maintenance of neuron functionality. The klp-4 (ok3537) allele results in a large, in frame deletion within the cargo-binding domain of the motor …

Single Nucleotide Polymorphism (Snps) Study On X-Chromosome In Thai Sle Populations, Krisana Jaiwan

Chulalongkorn University Theses and Dissertations (Chula ETD)

Systemic Lupus Erythematosus (SLE) is common autoimmune disease in Thailand which dominantly in females in ratio 9:1 of patients. Previous study has shown that the genetic components especially in X chromosome contributed a lot to the disease development. However, the susceptibility loci in Thai population have not been fully examined. Here, we conducted genome-wide association study (GWAS) on X chromosome using the data from two independent cohorts: primary dataset (controls = 1,683, SLE = 487) and secondary dataset (controls = 1,711, SLE = 455). Through meta-analyzing and imputation base on 1 KGP the two data set, SNP rs1059702 in IRAK1- …

Lamb Wool Shedding Is A Good Predictor Of Ewe Wool Shedding, Napoleón Vargas Jurado, Larry Kuehn, Ronald M. Lewis

Department of Animal Science: Faculty Publications

Interest in reducing labour costs due to shearing has led to development of breed types that shed their wool naturally. Selection at young ages can facilitate response. Reliability of predictions of adult from lamb wool shedding (WS) is thus key in the design of breeding programmes to increase shedding. Our objectives were to estimate heritabilities and genetic relationships between WS measured once in lambs and repeatedly in ewes and to assess the accuracy of lamb WS EBV to predict ewe WS EBV based on a multi‐trait threshold or a repeatability model. Data were 4,971 lamb and 3,335 ewe WS records …

Effect Of Ammoniation And Harvest Method On Waste And Consumption Of Corn Residue Bales Fed To Cows In A Round Bale Feeder, Ashley C. Conway, Zachary E. Carlson, Fred H. Hilscher Jr, J. C. Macdonald, Terry J. Klopfenstein, Mary E. Drewnoski

Department of Animal Science: Faculty Publications

To determine the effects of harvest method and ammoniation (3.7% of dry matter) on consumption and waste of baled corn residue, a 6 × 6 Latin square with a 3 × 2 factorial treatment structure was conducted. Six treatments consisted of either nonammoniated or ammoniated residue, harvested one of three ways: conventional rake and bale (CONV), New Holland Cornrower with two rows of stem chopped into the windrow with tailings (2ROW), or EZBale system (EZB) with a disengaged combine spreader and tailings dropped in a windrow. Open cows were grouped by body weight to produce a light block of two …

The Effects Of 2 Genetic Lines On Spatial Distribution And Use And Preference Of Perch And Nest Area In An Aviary System, Sheila E. Scheideler, Pamela E. Eusebio Balcazar, K. Hanford

Department of Animal Science: Faculty Publications

The objective of this trial was to evaluate spatial distribution, nest and perch usage, and preference of Lohmann Brown (BH) and Bovan White (WH) Leghorn hens raised in an aviary system. At 5 wk, 400 floor raised pullets, BH and WH strains, in equal numbers, were placed into 8 modified Big Dutchman Natura aviary units. Each aviary unit had 3 tiers with perches and an indoor litter area. At 25 wk, the number of birds was recorded by scan sampling every 4 h. The number of birds perching in each aviary unit was recorded every 4 h at 15, 25, …

Beef Cows With Atypical Estrous Cyclicity At Puberty Produced Calves With Deficits In Preweaning Muscling, Metabolic Indicators, And Myoblast Function But Not In Feedlot Performance, Rebecca M. Swanson, Rachel L. Gibbs, Caitlin Cadaret, Galen E. Erickson, Ty B. Schmidt, Andrea Cupp, Dustin T. Yates

Department of Animal Science: Faculty Publications

In cattle, age at puberty and number of estrous cycles prior to first breeding contribute to lifetime reproductive success (Perry et al., 1991). In our university beef herd, we have identified a subset of cows that exhibited irregular pubertal cyclicity patterns between weaning and their first breeding season, which we postulate is associated with high androstenedione in follicular fluid (Cupp et al., 2019). Cows with high androstenedione are subfertile but wean calves that average 17 kg heavier than the herd average (Summers et al., 2014). We hypothesized that this additional weight at weaning in their offspring is due to superior …

Deficits In Growth, Muscle Mass, And Body Composition Following Placental Insufficiency-Induced Intrauterine Growth Restriction Persisted In Lambs At 60 D Of Age But Were Improved By Daily Clenbuterol Supplementation, Rachel L. Gibbs, Rebecca M. Swanson, Joslyn K. Beard, Ty B. Schmidt, Jessica Lynn Petersen, Dustin T. Yates

Department of Animal Science: Faculty Publications

Low birthweight in livestock results from stress-induced intrauterine growth restriction (IUGR; Yates et al., 2018). IUGR fetuses exhibit diminished muscle growth that persists in the neonatal stage, leading to asymmetric body composition and decreased weight gain (Cadaret et al., 2019). Ultimately, low birthweight diminishes yield and carcass merit at harvest (Greenwood et al., 2000), making effective postnatal treatment strategies to improve IUGR growth outcomes necessary. In this study, we examined the benefits of injecting the β2 agonist clenbuterol daily to target adrenergic adaptations that we previously observed in IUGR muscle (Posont et al., 2018; Yates et al., 2018). We hypothesized …

Beta-Adrenergic Agonists Increase Maximal Output Of Oxidative Phosphorylation In Bovine Satellite Cells, Renae L. Sieck, Leah K. Treffer, Martonio Ponte Viana, Oleh Khalimonchuk, Ty B. Schmidt, Dustin T. Yates, Jessica L. Petersen

Department of Animal Science: Faculty Publications

Beta-adrenergic agonists (βAA), Ractopamine HCl (RH) and Zilpaterol HCl (ZH), are FDAapproved supplements utilized in pigs and cattle to improve growth performance, carcass weight, and longissimus muscle area (Arp et al., 2014; Lean et al., 2014). Previous studies within our group have focused on understanding molecular changes in skeletal muscle due to βAA supplementation. This work has shown that βAA supplementation increases glucose oxidation in muscle from thermoneutral and heat-stressed lambs (Barnes et al., 2019) and in rat skeletal muscle stimulated with ZH (Cadaret et al., 2017). Skeletal muscle transcriptomics of lambs supplemented ZH revealed upregulation of genes associated with …

Heat Stress And Β-Adrenergic Agonists Alter The Adipose Transcriptome And Fatty Acid Mobilization In Ruminant Livestock, Rachel R. Reith, Renae L. Sieck, Pablo C. Grijalva, Erin M. Duffy, Rebecca M. Swanson, Anna M. Fuller, Kristin A. Beede, Joslyn K. Beard, Duarte E. Diaz, Ty B. Schmidt, Dustin T. Yates, Jessica L. Petersen

Department of Animal Science: Faculty Publications

Growth and feed efficiency of cattle are improved by supplementation with the beta-adrenergic agonists (βAA), ractopamine hydrochloride (RH; β₁AA) or zilpaterol hydrochloride (ZH; β₂AA) (Elam et al., 2009). βAA supplementation alters adipose deposition by inhibiting fatty acid biosynthesis and promoting lipolysis of stored triacylglycerols into free fatty acids (FFAs) (Johnson et al., 2014). However, β₂ adrenoceptors (βAR) desensitize with chronic activation (Re et al., 1997); supplementation is thus limited to the last 20 to 40 d of feeding.

The annual economic impact of heat stress (HS) has been estimated to exceed $2.4 billion (St-Pierre et …

Bovine Respiratory Disease Influences On Nutrition And Nutrient Metabolism, Clinton R. Krehbiel

Department of Animal Science: Faculty Publications

• Inflammation caused by bovine respiratory disease (BRD) continues to be one of the greatest challenges facing beef cattle producers and feedlot managers.

• BRD results in decreased intake, daily gain, and feed efficiency in feedlot calves, decreasing growth rate and increasing required days on feed.

• Morbidity caused by BRD has been associated with decreased hot carcass weight and poor carcass characteristics.

• Acute phase protein production in the liver, initiated by proinflammatory cytokines, may shift the priority for amino acid and energy use by the host animal during periods of sickness.

• Nutrient requirements for stressed calves seem …

Commercial Genetic Testing For Type 2 Polysaccharide Storage Myopathy And Myofibrillar Myopathy Does Not Correspond To A Histopathological Diagnosis, Stephanie J. Valberg, C. J. Finno, Marisa L. Henry, Melissa Schott, Deborah Velez-Irizarry, Sichong Peng, Erica C. Mckenzie, Jessica L. Petersen

Department of Animal Science: Faculty Publications

Background: Commercial genetic tests for type 2 polysaccharide storage myopathy (PSSM2) and myofibrillar myopathy (MFM) have not been validated by peer-review, and formal regulation of veterinary genetic testing is lacking.

Objectives: To compare genotype and allele frequencies of commercial test variants (P variants) in MYOT (P2; rs1138656462), FLNC (P3a; rs1139799323), FLNC (P3b; rs1142918816) and MYOZ3 (P4; rs1142544043) between Warmblood (WB) and Arabian (AR) horses diagnosed with PSSM2/MFM by muscle histopathology, and phenotyped breed-matched controls. To quantify variant frequency in public repositories of ancient and modern horse breeds.

Study design: Cross sectional using archived clinical material and publicly available data.

Methods: …

Differential Longitudinal Establishment Of Human Fecal Bacterial Communities In Germ-Free Porcine And Murine Models, Nirosh Aluthge, Wesley A. Tom, Alison Bartenslager, Thomas E. Burkey, Phillip S. Miller, Kelly D. Heath, Craig Kreikemeier-Bower, Hatem Kittana, Robert Schmaltz, Amanda Ramer-Tait, Samodha Fernando

Department of Animal Science: Faculty Publications

The majority of microbiome studies focused on understanding mechanistic relationships between the host and the microbiota have used mice and other rodents as the model of choice. However, the domestic pig is a relevant model that is currently underutilized for human microbiome investigations. In this study, we performed a direct comparison of the engraftment of fecal bacterial communities from human donors between human microbiotaassociated (HMA) piglet and mouse models under identical dietary conditions. Analysis of 16S rRNA genes using amplicon sequence variants (ASVs) revealed that with the exception of early microbiota from infants, the more mature microbiotas tested established better …

Age Related Extracellular Matrix And Interstitial Cell Phenotype In Pulmonary Valves, Shaohua Wu, Vikas Kumar, Peng Xiao, Mitchell Kuss, Jung Yul Lim, Chittibabu Guda, Jonathan Butcher, Bin Duan

Department of Animal Science: Faculty Publications

Heart valve disease is a common manifestation of cardiovascular disease and is a significant cause of cardiovascular morbidity and mortality worldwide. The pulmonary valve (PV) is of primary concern because of its involvement in common congenital heart defects, and the PV is usually the site for prosthetic replacement following a Ross operation. Although effects of age on valve matrix components and mechanical properties for aortic and mitral valves have been studied, very little is known about the age-related alterations that occur in the PV. In this study, we isolated PV leaflets from porcine hearts in different age groups (~ 4–6 …

In Situ Analysis Of Line-1 Promoter Activity Using Lacz Transgenic Mice, Partha Sarathi Saha

Electronic Theses and Dissertations

Apart from an evolutionary role, transposable elements have been implicated in animal development and also in pathophysiology. Non-LTR retrotransposons– LINE-1, Alu and SVA - are responsible for over 120 cases of human genetic diseases as heritable insertions, and are emerging as an important etiological factor for cancer and neurological disorders as somatic mutations. It is estimated that among the total number of 500,000 LINE-1s presents in the human genome, 80-100 LINE-1s remain competent for retrotransposition. Retrotransposition is only possible when LINE-1 is expressed. Because LINE-1 transcription is regulated by its 5’UTR promoter, it is essential to understand the spatiotemporal control …

Functional Analysis Of Squamosa-Promoter Binding Protein Like 13 In Controlling Flowering Time, Plant Architecture, Grain Size, And Grain Number In Wheat, Ajay Gupta

Electronic Theses and Dissertations

Higher and stable yield is always a major objective of wheat genetic improvement programs. The SQUAMOSA-promoter binding protein-like (SPL) genes constitute a small family of plant-specific transcription factors with diverse functions in plant development and growth and have great potential in improving yield and other major agronomic traits. However, the functional characterization of the SPL gene family in wheat is far behind other cereal crops such as rice. Using phylogenetic analysis, we identified 56 wheat orthologues of rice SPL genes belonging to 19 homoeologous groups. Among these 19 orthologous TaSPL genes, nine harbor the micro RNA 156 recognition element (MRE) …

Examining Biodiversity Metrics And The Utility Of Dna Barcoding In The Northern Great Plains, Sarah Herzog

Electronic Theses and Dissertations

Due to heavy threats to remaining global floral and faunal diversity, it is imperative we can identify species and quantify ecosystem health to find best practices for land management and conservation. The tallgrass prairies of the Northern Great Plains are one example of a heavily imperiled ecosystem. The tallgrass prairies have been reduced to less one percent of their historical extent and are facing continued loss. Genetic approaches and evolutionary theory offer insights for identifying species and assessing how biodiversity metrics may correlate with ecosystem processes. My two projects aim to address two facets imperative to conservation in the tallgrass …

Development And Validation Of Gene Delivery Methods For ​Crassostrea Virginica, Adrienne N. Tracy

Honors Theses

The Eastern oyster (Crassostrea virginica) is an important part of the East Coastal USA economy because aquaculture creates jobs. Sadly, the oysters are under constant threat due to increasing pollution, red tides, and diseases. Bivalves, and oysters in particular, are also becoming potential model organisms in medical research. With the sequencing of the oyster genome, scientists are focusing on deciphering the function of the predicted genes. However, the limited number of molecular and cellular tools available makes functional annotation of the genome challenging. A consistent, replicable gene delivery system needs to be developed to assess gene function and understand the …

Characterization Of The Dyrk1a Protein-Protein Interaction Network, Varsha Ananthapadmanabhan

Theses and Dissertations

Human Dual specificity tyrosine (Y)-Regulated Kinase 1A (DYRK1A) is a protein kinase encoded by a dosage-dependent gene. An extra copy of DYRK1A contributes to Down syndrome (DS) pathogenesis while loss of one allele causes severe mental retardation and autism. DYRK1A is involved in phosphorylation of several proteins that regulate cell cycle control and tumor suppression. However, the function and regulation of this kinase is not well understood and current knowledge does not fully explain dosage-dependent function of this important kinase. Our previous proteomic studies identified several novel DYRK1A interacting proteins including RNF169, FAM117B, TROAP, LZTS1, LZTS2 and DCAF7. In this …

The Role Of Manganese In Streptococcus Sanguinis, Tanya M. Puccio

Theses and Dissertations

Streptococcus sanguinis is primarily associated with oral health as a commensal bacterium. As an opportunistic pathogen, S. sanguinis is capable of colonizing heart valve vegetations, leading to the disease infective endocarditis. Previous studies from our lab have identified the high-affinity manganese transporter SsaACB as important for endocarditis virulence. The impact that manganese depletion has on S. sanguinis had never been evaluated and a secondary manganese transporter has not been identified. Thus, we employed the use of a fermentor to control large-scale growth over time and depleted manganese in an ΔssaACB mutant using a metal chelator, EDTA. The changes in …